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. 2021 Sep;110(3):542-545.
doi: 10.1002/cpt.2321. Epub 2021 Jun 29.

Pharmacogene Variation Consortium: A Global Resource and Repository for Pharmacogene Variation

Andrea Gaedigk  1   2 , Scott T Casey  3 , Michelle Whirl-Carrillo  4 , Neil A Miller  3 , Teri E Klein  4   5
Affiliations

Pharmacogene Variation Consortium: A Global Resource and Repository for Pharmacogene Variation

Andrea Gaedigk et al. Clin Pharmacol Ther. 2021 Sep.
No abstract available

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Figures

Figure 1
Figure 1. PharmVar User Base
PharmVar is a resource that is globally (A) and nationally (B) utilized (data reflect usage between April 1, 2020 through March 29, 2021). The graded bar indicates number of users; user density is indicated by color intensity. User demographics excludes authors’ institutions to avoid counting PharmVar and PharmGKB site activities towards site use data.
Figure 2
Figure 2. Variation Window Redesigned to include HGVS annotations
The new Variation Window is exemplified for a variant that is present on numerous CYP2D6 haplotypes, or star alleles. The Variation Window is activated by clicking on a SNV on a gene page. The top portion of the Variation Window displays SNV coordinates according to HGVS nomenclature on the gene, transcript and genome (GRCh37 and GRCh38) levels. Coordinates are displayed as obtained through the NCBI Variation Services and are only manually curated if no results are returned. The middle portion displays SNV positions ‘PharmVar-style’ on the gene, transcript and genome (GRCh37 and GRCh38) levels listing positions for both count modes (sequence start and the ‘A’ of the ATG’ start codon being +1). Note that PharmVar consistently uses the 3’ Rule to determine the positions of inserted or deleted nucleotide(s) and thus, HGVS and ‘PharmVar-style’ positions may differ for insertion/deletion variants in some instances which is most likely explained by differences in sequence alignments. PharmVar also displays single nucleotide insertions as ‘ins’ while HGVS displays them as duplications or ‘dup’. Additional details and examples are provided in the PharmVar ‘Standards document’ (4). The bottom portion of the variation window provides a filter option to display all variants with the selected SNV, the link to dbSNP (if a rsID exists), as well as SNV frequency information. There is also a bar providing the option to display all haplotypes with the selected variant.
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References

    1. Desta Z et al. PharmVar GeneFocus: CYP2B6. Clin Pharmacol Ther, Epub Jan 15 (2021). - PMC - PubMed
    1. Botton MR et al. PharmVar GeneFocus: CYP2C19. Clin Pharmacol Ther 109, 352–66 (2021). - PMC - PubMed
    1. Nofziger C et al. PharmVar GeneFocus: CYP2D6. Clin Pharmacol Ther 107, 154–70 (2020). - PMC - PubMed
    1. PharmVar Standards https://www.pharmvar.org/genes.
    1. Yang JJ et al. Pharmacogene Variation Consortium Gene Introduction: NUDT15. Clin Pharmacol Ther 105, 1091–4 (2019). - PMC - PubMed

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